uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis
Class CDnaSpliceSiteAnalysis

java.lang.Object
  extended by uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
      extended by uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureAnalysis
          extended by uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.CDnaSpliceSiteAnalysis
All Implemented Interfaces:
BasicFeatureAnalysisAble

public class CDnaSpliceSiteAnalysis
extends FeatureAnalysis

Analysis class which calculates the high scoring path in a clustered sequence using a cDNA splice sites scoring system

Version:
1.0
Author:
Sebastian R. Spiegler

Constructor Summary
CDnaSpliceSiteAnalysis(java.util.ArrayList _arrListOfGMRegions, java.util.ArrayList _arrListOfCDnaRegions, SimpleArg _allArguments)
          constructor for CDnaSpliceSiteAnalysis objects
 
Method Summary
 java.util.ArrayList getHighScoringGmRegArr(java.util.ArrayList _arrListOfGMRegionsToAnalyze)
          method which returns the high scoring path of genemodels on a sequence using a cDNA splice site scoring system
 
Methods inherited from class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureAnalysis
getArrListOfFeatRegions
 
Methods inherited from class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
getAllArguments, getArrListOfGMRegions, getClassName
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

CDnaSpliceSiteAnalysis

public CDnaSpliceSiteAnalysis(java.util.ArrayList _arrListOfGMRegions,
                              java.util.ArrayList _arrListOfCDnaRegions,
                              SimpleArg _allArguments)
constructor for CDnaSpliceSiteAnalysis objects

Parameters:
_arrListOfGMRegions - ArrayList of genemodel regions
_arrListOfCDnaRegions - ArrayList of cDNA regions
_allArguments - SimpleArg object which contains all command line arguments
Method Detail

getHighScoringGmRegArr

public java.util.ArrayList getHighScoringGmRegArr(java.util.ArrayList _arrListOfGMRegionsToAnalyze)
method which returns the high scoring path of genemodels on a sequence using a cDNA splice site scoring system

Genemodel splice sites are scored with +1 when they match a cDNA splice site, with -1 when they overlap a cDNA but do not match and 0 when they do not overlap a cDNA. The total score is calculated as the sum of all splice site scores. For further details consult the documentation.

Specified by:
getHighScoringGmRegArr in interface BasicFeatureAnalysisAble
Specified by:
getHighScoringGmRegArr in class BasicFeatureAnalysis
Parameters:
_arrListOfGMRegionsToAnalyze - ArrayList of genemodel regions
Returns:
ArrayList of regions with high scoring genemodels